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Citations.bib
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@article{di2017nextflow,
title={Nextflow enables reproducible computational workflows},
author={Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
journal={Nature biotechnology},
volume={35},
number={4},
pages={316--319},
year={2017},
publisher={Nature Publishing Group}
}
@article{gruning2018bioconda,
title={Bioconda: sustainable and comprehensive software distribution for the life sciences},
author={Gr{\"u}ning, Bj{\"o}rn and Dale, Ryan and Sj{\"o}din, Andreas and Chapman, Brad A and Rowe, Jillian and Tomkins-Tinch, Christopher H and Valieris, Renan and K{\"o}ster, Johannes},
journal={Nature methods},
volume={15},
number={7},
pages={475--476},
year={2018},
publisher={Nature Publishing Group}
}
@article{zhu2019cut,
title={CUT\&RUNTools: a flexible pipeline for CUT\&RUN processing and footprint analysis},
author={Zhu, Qian and Liu, Nan and Orkin, Stuart H and Yuan, Guo-Cheng},
journal={Genome biology},
volume={20},
number={1},
pages={192},
year={2019},
publisher={Springer}
}
@article{meers2019peak,
title={Peak calling by Sparse Enrichment Analysis for CUT\&RUN chromatin profiling},
author={Meers, Michael P and Tenenbaum, Dan and Henikoff, Steven},
journal={Epigenetics \& chromatin},
volume={12},
number={1},
pages={42},
year={2019},
publisher={Springer}
}
@Manual{,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2017},
url = {https://www.R-project.org/},
}
@article{10.1093/bioinformatics/btx192,
author = {da Veiga Leprevost, Felipe and Grüning, Björn A and Alves Aflitos, Saulo and Röst, Hannes L and Uszkoreit, Julian and Barsnes, Harald and Vaudel, Marc and Moreno, Pablo and Gatto, Laurent and Weber, Jonas and Bai, Mingze and Jimenez, Rafael C and Sachsenberg, Timo and Pfeuffer, Julianus and Vera Alvarez, Roberto and Griss, Johannes and Nesvizhskii, Alexey I and Perez-Riverol, Yasset},
title = "{BioContainers: an open-source and community-driven framework for software standardization}",
journal = {Bioinformatics},
volume = {33},
number = {16},
pages = {2580-2582},
year = {2017},
month = {03},
abstract = "{BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters).The software is freely available at github.com/BioContainers/.}",
issn = {1367-4803},
doi = {10.1093/bioinformatics/btx192},
url = {https://doi.org/10.1093/bioinformatics/btx192},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/33/16/2580/25163480/btx192.pdf},
}
@article{langmead2012fast,
title={Fast gapped-read alignment with Bowtie 2},
author={Langmead, Ben and Salzberg, Steven L},
journal={Nature methods},
volume={9},
number={4},
pages={357},
year={2012},
publisher={Nature Publishing Group}
}
@article{kent2002human,
title={The human genome browser at UCSC},
author={Kent, W James and Sugnet, Charles W and Furey, Terrence S and Roskin, Krishna M and Pringle, Tom H and Zahler, Alan M and Haussler, David},
journal={Genome research},
volume={12},
number={6},
pages={996--1006},
year={2002},
publisher={Cold Spring Harbor Lab}
}
@article{li2009sequence,
title={The sequence alignment/map format and SAMtools},
author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
journal={Bioinformatics},
volume={25},
number={16},
pages={2078--2079},
year={2009},
publisher={Oxford University Press}
}
@misc{andrews2015quality,
title={A quality control tool for high throughput sequence data. 2010},
author={Andrews, Simon and FastQC, A},
year={2015}
}
@article{bolger2014trimmomatic,
title={Trimmomatic: a flexible trimmer for Illumina sequence data},
author={Bolger, Anthony M and Lohse, Marc and Usadel, Bjoern},
journal={Bioinformatics},
volume={30},
number={15},
pages={2114--2120},
year={2014},
publisher={Oxford University Press}
}
@article{quinlan2010bedtools,
title={BEDTools: a flexible suite of utilities for comparing genomic features},
author={Quinlan, Aaron R and Hall, Ira M},
journal={Bioinformatics},
volume={26},
number={6},
pages={841--842},
year={2010},
publisher={Oxford University Press}
}
@article{kent2010bigwig,
title={BigWig and BigBed: enabling browsing of large distributed datasets},
author={Kent, W James and Zweig, Ann S and Barber, G and Hinrichs, Angie S and Karolchik, Donna},
journal={Bioinformatics},
volume={26},
number={17},
pages={2204--2207},
year={2010},
publisher={Oxford University Press}
}
@article{zhang2008model,
title={Model-based analysis of ChIP-Seq (MACS)},
author={Zhang, Yong and Liu, Tao and Meyer, Clifford A and Eeckhoute, J{\'e}r{\^o}me and Johnson, David S and Bernstein, Bradley E and Nusbaum, Chad and Myers, Richard M and Brown, Myles and Li, Wei and others},
journal={Genome biology},
volume={9},
number={9},
pages={1--9},
year={2008},
publisher={BioMed Central}
}